Bioinformatics for Proteomics

Mass spectrometry based proteomics studies typically aim at measuring and comparing changes in biological samples. This however strongly relies on our ability to interpret the massive amounts of data produced by modern mass spectrometers. Therefore, methods and tools have been developed to tackle four major topics:

  1. Identification
  2. Functional Analysis
  3. Data Sharing
  4. Quantification

This tutorial aims at providing the basis for any user to go through the following workflow: (1) identify peptides, proteins and their modifications, (2) annotate the data with existing biological knowledge, and (3) share the data using online repositories. Finally, the different techniques for quantifying peptides and proteins will be introduced.

Notably, we will only employ user friendly and open source software. Despite our best efforts however, such software, or the resources they rely on, are not always available yet. For example, proteomics resources are heavily focused on a few model organisms, and working with data from other species is a lot more challenging.

Q&A: There are numerous questions listed throughout the chapters, highlighting important aspects of the diverse field of proteomics. Our suggested answers are available here.

Feedback: We would very much like to get your feedback on the tutorials. Please fill out our evaluation form. And if you encounter issues not tackled in the present tutorial, feel free to contact the authors directly.

Publication: If you like our tutorials please cite: Vaudel et al.: Shedding light on black boxes in protein identification. Proteomics. 2014 May;14(9):1001-5.

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